First of all , you cannot go switching protocols especially in the iPSCs , each one has a different target. For example , if you want to create integration free iPSCs then you can go with the proteins , mRNA , plasmids , episomal vectors... if you do not care about integration then you can go with yamanaka's ''recipie'', or the lentiviral system which offer greater efficiency.

I have personally used the lentiviral system and it worked fine.
If you can post your protocol , I'll be happy to pinpoint our differences.